
public interface SequenceAligner {

	public void setSequences(String str1, String str2);

	public boolean init();

	public void align();

	public void traceBack();

	public void setGapPenaltyFunction(GapPenalty function);

	public void setAlignmentScoreFunction(AlignmentScore function);

	public String getAlignedStr1();

	public String getAlignedStr2();

}